At the final whistle, Yamal stormed off the pitch and before then didn't celebrate Robert Lewandowski's 87th-minute goal that sealed the win.
Teammate Pau Cubarsi tried to calm down his teammate, but without success.
Flick then went to congratulate the Barcelona starlet, but Yamal said something that surprised the German coach.
On the way to the dressing room, Yamal was seen again gesturing and protesting with José Ramón de la Fuente, the Barca goalkeeping coach as he ushered him to the dressing room.
After the match, Flick said: "I think... I don't know exactly what it is, but in the end, as I said before, there was a lot of emotion in the game. And I mean, Lamine tried everything to score the second goal.
"That's perfect, that's great. And of course, not everything was perfect, but he tried everything. When he gets the ball, he's always available, and that's a good thing. And for me, that's how it is."
The German also said: "He tried everything to score the second goal, and that's fine. He tried everything. I think that's why he was angry."